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Magnesium in PDB 3csk: Structure of Dpp III From Saccharomyces Cerevisiae

Enzymatic activity of Structure of Dpp III From Saccharomyces Cerevisiae

All present enzymatic activity of Structure of Dpp III From Saccharomyces Cerevisiae:
3.4.14.4;

Protein crystallography data

The structure of Structure of Dpp III From Saccharomyces Cerevisiae, PDB code: 3csk was solved by P.K.Baral, N.Jajcanin, S.Deller, P.Macheroux, M.Abramic, K.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.621, 110.121, 67.908, 90.00, 113.45, 90.00
R / Rfree (%) 19.2 / 22.8

Other elements in 3csk:

The structure of Structure of Dpp III From Saccharomyces Cerevisiae also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Dpp III From Saccharomyces Cerevisiae (pdb code 3csk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Dpp III From Saccharomyces Cerevisiae, PDB code: 3csk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3csk

Go back to Magnesium Binding Sites List in 3csk
Magnesium binding site 1 out of 2 in the Structure of Dpp III From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Dpp III From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg713

b:49.1
occ:1.00
O A:HOH843 2.4 43.5 1.0
O A:LEU366 2.4 36.3 1.0
O A:HOH996 2.5 49.0 1.0
O A:HOH1027 2.5 61.3 1.0
O A:SER364 2.5 56.0 1.0
O A:TRP368 2.7 39.9 1.0
C A:SER364 3.4 47.0 1.0
C A:LEU366 3.6 37.4 1.0
C A:TRP368 3.8 42.1 1.0
O A:HOH855 3.8 43.1 1.0
N A:TRP368 3.9 41.0 1.0
O A:ILE363 3.9 38.6 1.0
N A:LEU366 4.0 37.8 1.0
CA A:SER364 4.0 45.7 1.0
CA A:LEU366 4.3 38.7 1.0
C A:LEU365 4.3 46.9 1.0
N A:LEU365 4.4 34.2 1.0
CA A:TRP368 4.4 44.7 1.0
N A:PRO367 4.6 39.6 1.0
CD1 A:TRP368 4.7 39.0 1.0
CB A:LEU366 4.7 33.3 1.0
CA A:LEU365 4.7 43.0 1.0
O A:LEU365 4.8 45.5 1.0
C A:ILE363 4.9 41.5 1.0
C A:PRO367 4.9 44.4 1.0
N A:SER369 4.9 46.3 1.0
N A:SER364 4.9 41.9 1.0
CG A:TRP368 4.9 40.2 1.0
CA A:PRO367 5.0 35.6 1.0
NE1 A:TRP368 5.0 35.8 1.0

Magnesium binding site 2 out of 2 in 3csk

Go back to Magnesium Binding Sites List in 3csk
Magnesium binding site 2 out of 2 in the Structure of Dpp III From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Dpp III From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg714

b:66.1
occ:1.00
O A:HOH975 2.1 53.4 1.0
O A:HOH1095 2.1 53.8 1.0
O A:HOH937 2.4 50.3 1.0
O A:HOH1051 2.4 54.8 1.0
O A:HOH1096 2.4 62.5 1.0
O A:HOH1097 2.6 62.4 1.0
OD2 A:ASP490 3.7 52.2 1.0
OD1 A:ASP490 3.9 52.6 1.0
CG A:ASP490 4.1 58.5 1.0
NE2 A:GLN645 4.5 55.0 1.0
O A:LYS492 4.5 44.5 1.0
O A:HOH1099 4.6 54.1 1.0
O A:PRO493 4.7 44.2 1.0
CA A:VAL494 4.7 43.1 1.0
O A:HOH767 4.8 35.5 1.0
CA A:GLY488 5.0 49.1 1.0

Reference:

P.K.Baral, N.Jajcanin-Jozic, S.Deller, P.Macheroux, M.Abramic, K.Gruber. The First Structure of Dipeptidyl-Peptidase III Provides Insight Into the Catalytic Mechanism and Mode of Substrate Binding. J.Biol.Chem. V. 283 22316 2008.
ISSN: ISSN 0021-9258
PubMed: 18550518
DOI: 10.1074/JBC.M803522200
Page generated: Mon Dec 14 08:02:16 2020

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